Why hasn't Batman ever said what had happened? He knows the story the Joker tells everyone about the chemicals. So why hasn't he denied it if it's not true?

That's how in Death Of The Family he knew it was Harley under the red hood, because she was relaying the same version of the story Joker told her about his origin. That Batman was responsible on that night he fell. But the truth is, Joker fell accidently or because he tried to escape.

Bruce has never denied nor confirmed the event however.

The story about the chemicals is just one of the many stories the Joker tells. He tells a different story each time so Batman has no reason to believe any of them at this point because he's heard a lot of them. Harley was told that same version. It's very much like the different scar stories in TDK.